I am having the same issue. I use a Thrustmaster T-Flight HOTAS X with Button 1 as the brake(apply/release) button with the repeat slider on extreme right. For my keyboard, it is the period(.) key. I also use FSUIPC.
I haven't read all the solutions posted here and I don't know if this solution has already been posted but the following steps solved my elevation issue.
Go to your FSX root folder (Generally C:/Program Files(x86)/Microsoft Games/Microsoft Flight Simulator X)>Scenery>0803>scenery>APX67250.bgl . All u need to do is rename this file to APX67250.bgl.off .
This solution worked for me except I get a small scenery overlap at the end of runway but at least now i don't drown into the runways
Hope this helps!